Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate Ga0059261_3754 Ga0059261_3754 Threonine dehydratase
Query= SwissProt::Q9WYJ1 (401 letters) >FitnessBrowser__Korea:Ga0059261_3754 Length = 322 Score = 186 bits (473), Expect = 6e-52 Identities = 110/294 (37%), Positives = 168/294 (57%), Gaps = 11/294 (3%) Query: 28 VLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSEEERKRGVVAASAGNHAQGVALAA 87 +++E+ G + K E LQ G+FKIRGA++++ + E+R++GVVA S+GNHAQGVA AA Sbjct: 29 LVAEIRGIPVMFKAECLQPIGAFKIRGAWHRLTAIDPEQREKGVVAFSSGNHAQGVAWAA 88 Query: 88 QIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNIFDEAYEAALRIQEKTGAVFVHPFN 147 + GIPA IVMP AP +K T LGA+V+ + ++ + A + GA V PF+ Sbjct: 89 KRLGIPAVIVMPADAPAAKRDSTLALGAEVVAYDRMKEDRVKIAAHLAHARGATLVPPFD 148 Query: 148 DPHVIAGQGTIGLEIMED-----LPDVEVVVVPVGGGGLISGVSVAIKSMNPEVKVIGVQ 202 DP +I GQG++ +E++ LPD +VVP GGGGL SGV++A+ PE + V+ Sbjct: 149 DPWIIEGQGSMAIEVLTQAAEMRLPDPGRIVVPCGGGGLASGVTLAL----PEAQTTIVE 204 Query: 203 TENMPSMIASLRRGRAERV--EGKPTLADGIAVKKPGDLTFELVKKYVDEMVAVNEEEIA 260 E M SL G E + PT D + +P LTF+++ + VAV+E E+ Sbjct: 205 PEGWDDMCRSLANGWIESIGESPPPTACDALQTFQPAQLTFDVLSRRGATGVAVSEAEVR 264 Query: 261 DAILFLLEQAKVVAEGAGAVGVAAVLNKLDVKGKKVAIVISGGNIDVNMIDRII 314 A + + ++V E GAV +AA+L +++SGGN D + R++ Sbjct: 265 AAQRWAARKLRLVVEPGGAVALAALLAGKVDPTPDTLVILSGGNADPDAYARVL 318 Lambda K H 0.317 0.136 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 242 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 322 Length adjustment: 29 Effective length of query: 372 Effective length of database: 293 Effective search space: 108996 Effective search space used: 108996 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory